1
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Jin X, Wang Y, Chen J, Niu M, Yang Y, Zhang Q, Bao G. Novel dual-targeting inhibitors of NSD2 and HDAC2 for the treatment of liver cancer: structure-based virtual screening, molecular dynamics simulation, and in vitro and in vivo biological activity evaluations. J Enzyme Inhib Med Chem 2024; 39:2289355. [PMID: 38059332 DOI: 10.1080/14756366.2023.2289355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/26/2023] [Indexed: 12/08/2023] Open
Abstract
Liver cancer exhibits a high degree of heterogeneity and involves intricate mechanisms. Recent research has revealed the significant role of histone lysine methylation and acetylation in the epigenetic regulation of liver cancer development. In this study, five inhibitors capable of targeting both histone lysine methyltransferase nuclear receptor-binding SET domain 2 (NSD2) and histone deacetylase 2 (HDAC2) were identified using a structure-based virtual screening approach. Notably, DT-NH-1 displayed a potent inhibition of NSD2 (IC50 = 0.08 ± 0.03 μM) and HDAC2 (IC50 = 5.24 ± 0.87 nM). DT-NH-1 also demonstrated a strong anti-proliferative activity against various liver cancer cell lines, particularly HepG2 cells, and exhibited a high level of biological safety. In an experimental xenograft model involving HepG2 cells, DT-NH-1 showed a significant reduction in tumour growth. Consequently, these findings indicate that DT-NH-1 will be a promising lead compound for the treatment of liver cancer with epigenetic dual-target inhibitors.
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Affiliation(s)
- Xing Jin
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yuting Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Jing Chen
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Miaomiao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Yang Yang
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Qiaoxuan Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guangyu Bao
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
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2
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Scheuerer S, Motlova L, Schäker-Hübner L, Sellmer A, Feller F, Ertl FJ, Koch P, Hansen FK, Barinka C, Mahboobi S. Biological and structural investigation of tetrahydro-β-carboline-based selective HDAC6 inhibitors with improved stability. Eur J Med Chem 2024; 276:116676. [PMID: 39067437 DOI: 10.1016/j.ejmech.2024.116676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/30/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024]
Abstract
Our previously reported HDAC6 inhibitor (HDAC6i) Marbostat-100 (4) has provided many arguments for further clinical evaluation. By the substitution of the acidic hydrogen of 4 for different carbon residues, we were able to generate an all-carbon stereocenter, which significantly improves the hydrolytic stability of the inhibitor. Further asymmetric synthesis has shown that the (S)-configured inhibitors preferentially bind to HDAC6. This led to the highly selective and potent methyl-substituted derivative S-29b, which elicited a long-lasting tubulin hyperacetylation in MV4-11 cells. Finally, a crystal structure of the HDAC6/S-29b complex provided mechanistic explanation for the high potency and stereoselectivity of synthesized compound series.
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Affiliation(s)
- Simon Scheuerer
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry I, University of Regensburg, 93040, Regensburg, Germany
| | - Lucia Motlova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Linda Schäker-Hübner
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn, 53121, Bonn, Germany
| | - Andreas Sellmer
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry I, University of Regensburg, 93040, Regensburg, Germany
| | - Felix Feller
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn, 53121, Bonn, Germany
| | - Fabian J Ertl
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry II, University of Regensburg, 93040, Regensburg, Germany
| | - Pierre Koch
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry II, University of Regensburg, 93040, Regensburg, Germany
| | - Finn K Hansen
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn, 53121, Bonn, Germany
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Siavosh Mahboobi
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry I, University of Regensburg, 93040, Regensburg, Germany.
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3
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Carullo G, Orsini N, Piano I, Pozzetti L, Papa A, Fontana A, Napoli D, Corsi F, Marco BD, Galante A, Marotta L, Panzeca G, O'Brien J, Sanchez AG, Doherty H, Mahon N, Clarke L, Contri C, Pasquini S, Gorelli B, Saponara S, Valoti M, Vincenzi F, Varani K, Ramunno A, Brogi S, Butini S, Gemma S, Kennedy BN, Gargini C, Strettoi E, Campiani G. Targeting Relevant HDACs to Support the Survival of Cone Photoreceptors in Inherited Retinal Diseases: Identification of a Potent Pharmacological Tool with In Vitro and In Vivo Efficacy. J Med Chem 2024; 67:14946-14973. [PMID: 38961727 DOI: 10.1021/acs.jmedchem.4c00477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Inherited retinal diseases, which include retinitis pigmentosa, are a family of genetic disorders characterized by gradual rod-cone degeneration and vision loss, without effective pharmacological treatments. Experimental approaches aim to delay disease progression, supporting cones' survival, crucial for human vision. Histone deacetylases (HDACs) mediate the activation of epigenetic and nonepigenetic pathways that modulate cone degeneration in RP mouse models. We developed new HDAC inhibitors (5a-p), typified by a tetrahydro-γ-carboline scaffold, characterized by high HDAC6 inhibition potency with balanced physicochemical properties for in vivo studies. Compound 5d (repistat, IC50 HDAC6 = 6.32 nM) increased the levels of acetylated α-tubulin compared to histone H3 in ARPE-19 and 661W cells. 5d promoted vision rescue in the atp6v0e1-/- zebrafish model of photoreceptor dysfunction. A single intravitreal injection of 5d in the rd10 mouse model of RP supported morphological and functional preservation of cone cells and maintenance of the retinal pigment epithelium array.
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Affiliation(s)
- Gabriele Carullo
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Noemi Orsini
- Neuroscience Institute, Italian National Research Council (CNR) Area della Ricerca, Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
- Regional Doctorate School in Neuroscience of Universities of Florence, Pisa, Siena, Florence, CNR Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
| | - Ilaria Piano
- Department of Pharmacy, Via Bonanno 6, 56124 Pisa, Italy
| | - Luca Pozzetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Alessandro Papa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Anna Fontana
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Debora Napoli
- Neuroscience Institute, Italian National Research Council (CNR) Area della Ricerca, Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
- Regional Doctorate School in Neuroscience of Universities of Florence, Pisa, Siena, Florence, CNR Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
| | | | - Beatrice Di Marco
- Neuroscience Institute, Italian National Research Council (CNR) Area della Ricerca, Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
- Regional Doctorate School in Neuroscience of Universities of Florence, Pisa, Siena, Florence, CNR Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
| | | | - Ludovica Marotta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Giovanna Panzeca
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Justine O'Brien
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Alicia Gomez Sanchez
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Harry Doherty
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Niamh Mahon
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Leni Clarke
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Chiara Contri
- Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 17-19, 44121 Ferrara, Italy
| | - Silvia Pasquini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Fossato di Mortara 17-19, 44121 Ferrara, Italy
| | - Beatrice Gorelli
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Simona Saponara
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Massimo Valoti
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Fabrizio Vincenzi
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Fossato di Mortara 17-19, 44121 Ferrara, Italy
| | - Katia Varani
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Fossato di Mortara 17-19, 44121 Ferrara, Italy
| | - Anna Ramunno
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84100 Fisciano (SA), Italy
| | - Simone Brogi
- Department of Pharmacy, Via Bonanno 6, 56124 Pisa, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Breandán N Kennedy
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | | | - Enrica Strettoi
- Neuroscience Institute, Italian National Research Council (CNR) Area della Ricerca, Via Giuseppe Moruzzi 1, 56124 Pisa, Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-7346, Iran
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4
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Liang T, Liu S, Dang B, Luan X, Guo Y, Steimbach RR, Hu J, Lu L, Yue P, Wang R, Zheng M, Gao J, Yin X, Chen X. Multimechanism biological profiling of tetrahydro-β-carboline analogues as selective HDAC6 inhibitors for the treatment of Alzheimer's disease. Eur J Med Chem 2024; 275:116624. [PMID: 38925015 DOI: 10.1016/j.ejmech.2024.116624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/08/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
With the intensive research on the pathogenesis of Alzheimer's disease (AD), inhibition of HDAC6 appears to be a potential therapeutic approach for AD. In this paper, a series of tetrahydro-β-carboline derivatives with hydroxamic acid group were fast synthesized. Among all, the most potent 15 selectively inhibited HDAC6 with IC50 of 15.2 nM and markedly increased acetylated alpha-tubulin levels. In cellular assay, 15 showed excellent neurotrophic effect by increasing the expression of GAP43 and Beta-3 tubulin markers. Besides, 15 showed neuroprotective effects in PC12 or SH-SY5Y cells against H2O2 and 6-OHDA injury through activation of Nrf2, catalase and Prx II, and significantly reduced H2O2-induced reactive oxygen species (ROS) production. In vivo, 15 significantly attenuated zebrafish anxiety-like behaviour and memory deficits in a SCOP-induced zebrafish model of AD. To sum up, multifunctional 15 might be a good lead to develop novel tetrahydrocarboline-based agents for the treatment of AD.
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Affiliation(s)
- Ting Liang
- Shaanxi Key Labotory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, PR China
| | - Shiru Liu
- Shaanxi Key Labotory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, PR China
| | - Baiyun Dang
- Shaanxi Key Labotory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, PR China
| | - Xiaofa Luan
- Shaanxi Key Labotory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, PR China
| | - Yifan Guo
- Shaanxi Key Labotory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, PR China
| | - Raphael R Steimbach
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany; Biosciences Faculty, University of Heidelberg, 69120, Heidelberg, Germany
| | - Jiadong Hu
- School of Medicinal and Chemical Engineering, Yangling Vocational & Technical College, Yangling, 712100, PR China
| | - Long Lu
- School of Medicinal and Chemical Engineering, Yangling Vocational & Technical College, Yangling, 712100, PR China
| | - Peiyu Yue
- School of Medicinal and Chemical Engineering, Yangling Vocational & Technical College, Yangling, 712100, PR China
| | - Ruotian Wang
- School of Medicinal and Chemical Engineering, Yangling Vocational & Technical College, Yangling, 712100, PR China
| | - Meng Zheng
- Shaanxi Key Labotory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, PR China
| | - Jinming Gao
- Shaanxi Key Labotory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, PR China.
| | - Xia Yin
- Shaanxi Key Labotory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, PR China.
| | - Xin Chen
- Shaanxi Key Labotory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, PR China.
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5
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Gu Z, Lin S, Yu J, Jin F, Zhang Q, Xia K, Chen L, Li Y, He B. Advances in dual-targeting inhibitors of HDAC6 for cancer treatment. Eur J Med Chem 2024; 275:116571. [PMID: 38857566 DOI: 10.1016/j.ejmech.2024.116571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
Histone Deacetylase 6 (HDAC6) is an essential regulator of histone acetylation processes, exerting influence on a multitude of cellular functions such as cell motility, endocytosis, autophagy, apoptosis, and protein trafficking through its deacetylation activity. The significant implications of HDAC6 in diseases such as cancer, neurodegenerative disorders, and immune disorders have motivated extensive investigation into the development of specific inhibitors targeting this enzyme for therapeutic purposes. Single targeting drugs carry the risk of inducing drug resistance, thus prompting exploration of dual targeting therapy which offers the potential to impact multiple signaling pathways simultaneously, thereby lowering the likelihood of resistance development. While pharmacological studies have exhibited promise in combined therapy involving HDAC6, challenges related to potential drug interactions exist. In response to these challenges, researchers are investigating HDAC6 hybrid molecules which enable the concomitant targeting of HDAC6 and other key proteins, thus enhancing treatment efficacy while mitigating side effects and reducing the risk of resistance compared to traditional combination therapies. The published design strategies for dual targeting inhibitors of HDAC6 are summarized and discussed in this review. This will provide some valuable insights into more novel HDAC6 dual targeting inhibitors to meet the urgent need for innovative therapies in oncology and other related fields.
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Affiliation(s)
- Zhicheng Gu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang, 550004, China
| | - Shuxian Lin
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang, 550004, China; Department of Pharmacy, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Junhui Yu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang, 550004, China
| | - Fei Jin
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang, 550004, China
| | - Qingqing Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang, 550004, China
| | - Keli Xia
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang, 550004, China
| | - Lei Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang, 550004, China
| | - Yan Li
- School of Basic Medical Science, Guizhou Medical University, Guiyang, Guizhou, 550004, China
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang, 550004, China.
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6
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Asmamaw MD, He A, Zhang LR, Liu HM, Gao Y. Histone deacetylase complexes: Structure, regulation and function. Biochim Biophys Acta Rev Cancer 2024; 1879:189150. [PMID: 38971208 DOI: 10.1016/j.bbcan.2024.189150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 06/07/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
Histone deacetylases (HDACs) are key epigenetic regulators, and transcriptional complexes with deacetylase function are among the epigenetic corepressor complexes in the nucleus that target the epigenome. HDAC-bearing corepressor complexes such as the Sin3 complex, NuRD complex, CoREST complex, and SMRT/NCoR complex are common in biological systems. These complexes activate the otherwise inactive HDACs in a solitary state. HDAC complexes play vital roles in the regulation of key biological processes such as transcription, replication, and DNA repair. Moreover, deregulated HDAC complex function is implicated in human diseases including cancer. Therapeutic strategies targeting HDAC complexes are being sought actively. Thus, illustration of the nature and composition of HDAC complexes is vital to understanding the molecular basis of their functions under physiologic and pathologic conditions, and for designing targeted therapies. This review presents key aspects of large multiprotein HDAC-bearing complexes including their structure, function, regulatory mechanisms, implication in disease development, and role in therapeutics.
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Affiliation(s)
- Moges Dessale Asmamaw
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Ang He
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Li-Rong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
| | - Hong-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
| | - Ya Gao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
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7
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Carreiras MDC, Marco-Contelles J. Hydrazides as Inhibitors of Histone Deacetylases. J Med Chem 2024; 67:13512-13533. [PMID: 39092855 DOI: 10.1021/acs.jmedchem.4c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
In this Perspective, we have brought together available biological evidence on hydrazides as histone deacetylase inhibitors (HDACis) and as a distinct type of Zn-binding group (ZBG) to be reviewed for the first time in the literature. N-Alkyl hydrazides have transformed the field, providing innovative and practical chemical tools for selective and effective inhibition of specific histone deacetylase (HDAC) enzymes, in addition to the usual hydroxamic acid and o-aminoanilide ZBG-bearing HDACis. This has enabled efficient targeting of neurodegenerative diseases such as Alzheimer's disease, cancer, cardiovascular diseases, and protozoal pathologies.
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Affiliation(s)
- Maria do Carmo Carreiras
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - José Marco-Contelles
- Laboratory of Medicinal Chemistry, Institute of Organic Chemistry CSIC, Juan de la Cierva, 3, 28006 Madrid, Spain
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8
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Yang FF, Liu JJ, Xu XL, Hu T, Liu JQ, He ZX, Zhao GY, Wei B, Ma LY. Discovery of Novel Imidazo[1,2- a]pyridine-Based HDAC6 Inhibitors as an Anticarcinogen with a Cardioprotective Effect. J Med Chem 2024; 67:14345-14369. [PMID: 39102466 DOI: 10.1021/acs.jmedchem.4c01168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Cardiotoxicity associated with chemotherapy has gradually become the major cause of death in cancer patients. The development of bifunctional drugs with both cardioprotective and antitumor effects has become the future direction. HDAC6 plays important roles in the progression, treatment, and prognosis of cancer and cardiovascular diseases, but bifunctional inhibitors have not been reported. Herein, structure-activity relationship studies driven by pharmacophore-based remodification and fragment-based design were performed to yield highly potent HDAC6 inhibitor I-c4 containing imidazo[1,2-a]pyridine. Importantly, I-c4 effectively suppressed the growth of MGC-803 xenografts in vitro and in vivo by inhibiting the deacetylation pathway without causing myocardial damage after long-term administration. Meanwhile, I-c4 could mitigate severe myocardial damage against H2O2 or myocardial ischemia/reperfusion in vitro and in vivo. Further studies revealed that the cardioprotective effect of I-c4 was associated with reduction of inflammatory cytokines. Taken together, I-c4 may represent a novel lead compound for further development of an anticarcinogen with a cardioprotective effect.
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Affiliation(s)
- Fei-Fei Yang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, China
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China
| | - Jing-Jing Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, China
| | - Xue-Li Xu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, China
| | - Ting Hu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, China
| | - Jian-Quan Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, China
| | - Zhang-Xu He
- School of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China
| | - Guang-Yuan Zhao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, China
| | - Bo Wei
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, China
| | - Li-Ying Ma
- State Key Laboratory of Esophageal Cancer Prevention and Treatment; Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, China
- China Meheco Topfond Pharmaceutical Co.; Key Laboratory of Cardio-cerebrovascular Drug, Zhumadian 463000, China
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9
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Zhao C, Zhang J, Zhou H, Setroikromo R, Poelarends GJ, Dekker FJ. Exploration of Hydrazide-Based HDAC8 PROTACs for the Treatment of Hematological Malignancies and Solid Tumors. J Med Chem 2024; 67:14016-14039. [PMID: 39089850 PMCID: PMC11345830 DOI: 10.1021/acs.jmedchem.4c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/25/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024]
Abstract
HDAC8 can mediate signals by using its enzymatic or nonenzymatic functions, which are expected to be critical for various types of cancer. Herein, we employed proteolysis targeting chimera (PROTAC) technology to target the enzymatic as well as the nonenzymatic functions of HDAC8. A potent and selective HDAC8 PROTAC Z16 (CZH-726) with low nanomolar DC50 values in various cell lines was identified. Interestingly, Z16 induced structural maintenance of chromosomes protein 3 (SMC3) hyperacetylation at low concentrations and histone hyperacetylation at high concentrations, which can be explained by HDAC8 degradation and off-target HDAC inhibition, respectively. Notably, Z16 potently inhibited proliferation of various cancer cell lines and the antiproliferative mechanisms proved to be cell-type-dependent, which, to a large extent, is due to off-target HDAC inhibition. In conclusion, we report a hydrazide-based HDAC8 PROTAC Z16, which can be used as a probe to investigate the biological functions of HDAC8.
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Affiliation(s)
| | | | - Hangyu Zhou
- Department of Chemical and Pharmaceutical
Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical
Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Gerrit J. Poelarends
- Department of Chemical and Pharmaceutical
Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical
Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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10
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Mert NM, Erdogan B, Yelekçi K. Repurposing of known drugs from multiple libraries to identify novel and potential selective inhibitors of HDAC6 via in silico approach and molecular modeling. Heliyon 2024; 10:e35020. [PMID: 39157373 PMCID: PMC11328036 DOI: 10.1016/j.heliyon.2024.e35020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 08/20/2024] Open
Abstract
Histone deacetylase 6 (HDAC6, Class IIb) is a promising target for anticancer drugs. So far, few nonselective HDAC inhibitors have received regulatory approval as anticancer agents. However, they are associated with cell toxicity. Thus, isoform-selective inhibitors may be desirable. Here, we conducted structure-based virtual screening of multiple libraries containing a total of 2,250,135 compounds against HDAC6. The top hits with good docking scores and potential selectivity over HDAC10 (Class IIb) were submitted to 100 ns molecular dynamics simulation to monitor their dynamic behaviors and stability in the binding pockets of these enzymes. Furthermore, the drug-likeness and ADMET properties of these hits were estimated computationally. Four diverse compounds from different sources, including NCI and ZINC databases (BDH33926500, CID667061, Cromolyn, and ZINC000103531486), show potential selectivity for HDAC6.
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Affiliation(s)
- Naz Mina Mert
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Cibali, Istanbul, Turkey
| | - Buse Erdogan
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Cibali, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Cibali, Istanbul, Turkey
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11
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Pinzi L, Belluti S, Piccinini I, Imbriano C, Rastelli G. Searching for Novel HDAC6/Hsp90 Dual Inhibitors with Anti-Prostate Cancer Activity: In Silico Screening and In Vitro Evaluation. Pharmaceuticals (Basel) 2024; 17:1072. [PMID: 39204176 PMCID: PMC11357446 DOI: 10.3390/ph17081072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/10/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Prostate cancer (PCA) is one of the most prevalent types of male cancers. While current treatments for early-stage PCA are available, their efficacy is limited in advanced PCA, mainly due to drug resistance or low efficacy. In this context, novel valuable therapeutic opportunities may arise from the combined inhibition of histone deacetylase 6 (HDAC6) and heat shock protein 90 (Hsp90). These targets are mutually involved in the regulation of several processes in cancer cells, and their inhibition is demonstrated to provide synergistic effects against PCA. On these premises, we performed an extensive in silico virtual screening campaign on commercial compounds in search of dual inhibitors of HDAC6 and Hsp90. In vitro tests against recombinant enzymes and PCA cells with different levels of aggressiveness allowed the identification of a subset of compounds with inhibitory activity against HDAC6 and antiproliferative effects towards LNCaP and PC-3 cells. None of the candidates showed appreciable Hsp90 inhibition. However, the discovered compounds have low molecular weight and a chemical structure similar to that of potent Hsp90 blockers. This provides an opportunity for structural and medicinal chemistry optimization in order to obtain HDAC6/Hsp90 dual modulators with antiproliferative effects against prostate cancer. These findings were discussed in detail in the study.
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Affiliation(s)
| | | | | | | | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy; (L.P.); (S.B.); (I.P.); (C.I.)
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12
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Pradel LS, Ho YL, Gohlke H, Kassack MU. The Antioxidant and HDAC-Inhibitor α-Lipoic Acid Is Synergistic with Exemestane in Estrogen Receptor-Positive Breast Cancer Cells. Int J Mol Sci 2024; 25:8455. [PMID: 39126024 PMCID: PMC11313180 DOI: 10.3390/ijms25158455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Anti-estrogenic therapy is established in the management of estrogen receptor (ER)-positive breast cancer. However, to overcome resistance and improve therapeutic outcome, novel strategies are needed such as targeting widely recognized aberrant epigenetics. The study aims to investigate the combination of the aromatase inhibitor exemestane and the histone deacetylase (HDAC) inhibitor and antioxidant α-lipoic acid in ER-positive breast cancer cells. First, the enantiomers and the racemic mixture of α-lipoic acid, and rac-dihydro-lipoic acid were investigated for HDAC inhibition. We found HDAC inhibitory activity in the 1-3-digit micromolar range with a preference for HDAC6. Rac-dihydro-lipoic acid is slightly more potent than rac-α-lipoic acid. The antiproliferative IC50 value of α-lipoic acid is in the 3-digit micromolar range. Notably, the combination of exemestane and α-lipoic acid resulted in synergistic behavior under various incubation times (24 h to 10 d) and readouts (MTT, live-cell fluorescence microscopy, caspase activation) analyzed by the Chou-Talalay method. α-lipoic acid increases mitochondrial fusion and the expression of apoptosis-related proteins p21, APAF-1, BIM, FOXO1, and decreases expression of anti-apoptotic proteins survivin, BCL-2, and c-myc. In conclusion, combining exemestane with α-lipoic acid is a promising novel treatment option for ER-positive breast cancer.
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Affiliation(s)
- Laura S. Pradel
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (L.S.P.); (Y.-L.H.); (H.G.)
| | - Yu-Lin Ho
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (L.S.P.); (Y.-L.H.); (H.G.)
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (L.S.P.); (Y.-L.H.); (H.G.)
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Matthias U. Kassack
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (L.S.P.); (Y.-L.H.); (H.G.)
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13
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San José-Enériz E, Gimenez-Camino N, Rabal O, Garate L, Miranda E, Gómez-Echarte N, García F, Charalampopoulou S, Sáez E, Vilas-Zornoza A, San Martín-Uriz P, Valcárcel LV, Barrena N, Alignani D, Tamariz-Amador LE, Pérez-Ruiz A, Hilscher S, Schutkowski M, Alfonso-Pierola A, Martinez-Calle N, Larrayoz MJ, Paiva B, Calasanz MJ, Muñoz J, Isasa M, Martin-Subero JI, Pineda-Lucena A, Oyarzabal J, Agirre X, Prósper F. Epigenetic-based differentiation therapy for Acute Myeloid Leukemia. Nat Commun 2024; 15:5570. [PMID: 38956053 PMCID: PMC11219871 DOI: 10.1038/s41467-024-49784-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/18/2024] [Indexed: 07/04/2024] Open
Abstract
Despite the development of novel therapies for acute myeloid leukemia, outcomes remain poor for most patients, and therapeutic improvements are an urgent unmet need. Although treatment regimens promoting differentiation have succeeded in the treatment of acute promyelocytic leukemia, their role in other acute myeloid leukemia subtypes needs to be explored. Here we identify and characterize two lysine deacetylase inhibitors, CM-444 and CM-1758, exhibiting the capacity to promote myeloid differentiation in all acute myeloid leukemia subtypes at low non-cytotoxic doses, unlike other commercial histone deacetylase inhibitors. Analyzing the acetylome after CM-444 and CM-1758 treatment reveals modulation of non-histone proteins involved in the enhancer-promoter chromatin regulatory complex, including bromodomain proteins. This acetylation is essential for enhancing the expression of key transcription factors directly involved in the differentiation therapy induced by CM-444/CM-1758 in acute myeloid leukemia. In summary, these compounds may represent effective differentiation-based therapeutic agents across acute myeloid leukemia subtypes with a potential mechanism for the treatment of acute myeloid leukemia.
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Affiliation(s)
- Edurne San José-Enériz
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Naroa Gimenez-Camino
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Obdulia Rabal
- Small-Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Leire Garate
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Estibaliz Miranda
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Nahia Gómez-Echarte
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Fernando García
- ProteoRed-ISCIII, Unidad de Proteómica, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Stella Charalampopoulou
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Casanova 143, 08036, Barcelona, Spain
| | - Elena Sáez
- Small-Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Amaia Vilas-Zornoza
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Patxi San Martín-Uriz
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Luis V Valcárcel
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
- TECNUN, Universidad de Navarra, Manuel de Lardizábal 13, 20018, San Sebastián, Spain
| | - Naroa Barrena
- TECNUN, Universidad de Navarra, Manuel de Lardizábal 13, 20018, San Sebastián, Spain
| | - Diego Alignani
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Luis Esteban Tamariz-Amador
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
- Departmento de Hematología, Clínica Universidad de Navarra, and CCUN, Universidad de Navarra, Avenida Pío XII 36, 31008, Pamplona, Spain
| | - Ana Pérez-Ruiz
- Biomedical Engineering Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Sebastian Hilscher
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | - Mike Schutkowski
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | - Ana Alfonso-Pierola
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
- Departmento de Hematología, Clínica Universidad de Navarra, and CCUN, Universidad de Navarra, Avenida Pío XII 36, 31008, Pamplona, Spain
| | - Nicolás Martinez-Calle
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
- Departmento de Hematología, Clínica Universidad de Navarra, and CCUN, Universidad de Navarra, Avenida Pío XII 36, 31008, Pamplona, Spain
| | - María José Larrayoz
- CIMA LAB Diagnostics, Universidad de Navarra, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Bruno Paiva
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
| | - María José Calasanz
- CIMA LAB Diagnostics, Universidad de Navarra, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Javier Muñoz
- Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009, Bilbao, Spain
| | - Marta Isasa
- ProteoRed-ISCIII, Unidad de Proteómica, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - José Ignacio Martin-Subero
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Casanova 143, 08036, Barcelona, Spain
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys 23, 08010, Barcelona, Spain
| | - Antonio Pineda-Lucena
- Small-Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Julen Oyarzabal
- Small-Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, Avenida Pío XII 55, 31008, Pamplona, Spain.
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain.
| | - Felipe Prósper
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain.
- Departmento de Hematología, Clínica Universidad de Navarra, and CCUN, Universidad de Navarra, Avenida Pío XII 36, 31008, Pamplona, Spain.
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14
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Diniz LP, Morgado J, Bergamo Araujo AP, da Silva Antônio LM, Mota-Araujo HP, de Sena Murteira Pinheiro P, Sagrillo FS, Cesar GV, Ferreira ST, Figueiredo CP, Manssour Fraga CA, Gomes FCA. Histone deacetylase inhibition mitigates cognitive deficits and astrocyte dysfunction induced by amyloid-β (Aβ) oligomers. Br J Pharmacol 2024. [PMID: 38936407 DOI: 10.1111/bph.16439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND AND PURPOSE Inhibitors of histone deacetylases (iHDACs) are promising drugs for neurodegenerative diseases. We have evaluated the therapeutic potential of the new iHDAC LASSBio-1911 in Aβ oligomer (AβO) toxicity models and astrocytes, key players in neuroinflammation and Alzheimer's disease (AD). EXPERIMENTAL APPROACH Astrocyte phenotype and synapse density were evaluated by flow cytometry, Western blotting, immunofluorescence and qPCR, in vitro and in mice. Cognitive function was evaluated by behavioural assays using a mouse model of intracerebroventricular infusion of AβO. KEY RESULTS LASSBio-1911 modulates reactivity and synaptogenic potential of cultured astrocytes and improves synaptic markers in cultured neurons and in mice. It prevents AβO-triggered astrocytic reactivity in mice and enhances the neuroprotective potential of astrocytes. LASSBio-1911 improves behavioural performance and rescues synaptic and memory function in AβO-infused mice. CONCLUSION AND IMPLICATIONS These results contribute to unveiling the mechanisms underlying astrocyte role in AD and provide the rationale for using astrocytes as targets to new drugs for AD.
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Affiliation(s)
- Luan Pereira Diniz
- Laboratório de Neurobiologia Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana Morgado
- Laboratório de Neurobiologia Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Paula Bergamo Araujo
- Laboratório de Neurobiologia Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda Savacini Sagrillo
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriele Vargas Cesar
- Laboratório de Neurobiologia Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sérgio T Ferreira
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flávia Carvalho Alcantara Gomes
- Laboratório de Neurobiologia Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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15
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Santini A, Tassinari E, Poeta E, Loi M, Ciani E, Trazzi S, Piccarducci R, Daniele S, Martini C, Pagliarani B, Tarozzi A, Bersani M, Spyrakis F, Danková D, Olsen CA, Soldati R, Tumiatti V, Montanari S, De Simone A, Milelli A. First in Class Dual Non-ATP-Competitive Glycogen Synthase Kinase 3β/Histone Deacetylase Inhibitors as a Potential Therapeutic to Treat Alzheimer's Disease. ACS Chem Neurosci 2024; 15:2099-2111. [PMID: 38747979 DOI: 10.1021/acschemneuro.4c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
Despite recent FDA approvals, Alzheimer's disease (AD) still represents an unmet medical need. Among the different available therapeutic approaches, the development of multitarget molecules represents one of the most widely pursued. In this work, we present a second generation of dual ligands directed toward highly networked targets that are deeply involved in the development of the disease, namely, Histone Deacetylases (HDACs) and Glycogen Synthase Kinase 3β (GSK-3β). The synthesized compounds are highly potent GSK-3β, HDAC2, and HDAC6 inhibitors with IC50 values in the nanomolar range of concentrations. Among them, compound 4 inhibits histone H3 and tubulin acetylation at 0.1 μM concentration, blocks hyperphosphorylation of tau protein, and shows interesting immunomodulatory and neuroprotective properties. These features, together with its ability to cross the blood-brain barrier and its favorable physical-chemical properties, make compound 4 a promising hit for the development of innovative disease-modifying agents.
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Affiliation(s)
- Alan Santini
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Elisa Tassinari
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Eleonora Poeta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Francesco Selmi 3, 40126 Bologna, Italy
| | - Manuela Loi
- Department of Biomedical and Neuromotor Science, Alma Mater Studiorum-University of Bologna, Piazza di Porta S. Donato, 2, 40126 Bologna, Italy
| | - Elisabetta Ciani
- Department of Biomedical and Neuromotor Science, Alma Mater Studiorum-University of Bologna, Piazza di Porta S. Donato, 2, 40126 Bologna, Italy
| | - Stefania Trazzi
- Department of Biomedical and Neuromotor Science, Alma Mater Studiorum-University of Bologna, Piazza di Porta S. Donato, 2, 40126 Bologna, Italy
| | - Rebecca Piccarducci
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 6, 56126 Pisa, Italy
| | - Simona Daniele
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 6, 56126 Pisa, Italy
| | - Claudia Martini
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 6, 56126 Pisa, Italy
| | - Barbara Pagliarani
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Andrea Tarozzi
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Matteo Bersani
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy
| | - Daniela Danková
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
| | - Roberto Soldati
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Vincenzo Tumiatti
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Serena Montanari
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Angela De Simone
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy
| | - Andrea Milelli
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
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Tretbar M, Schliehe-Diecks J, von Bredow L, Tan K, Roatsch M, Tu JW, Kemkes M, Sönnichsen M, Schöler A, Borkhardt A, Bhatia S, Hansen FK. Preferential HDAC6 inhibitors derived from HPOB exhibit synergistic antileukemia activity in combination with decitabine. Eur J Med Chem 2024; 272:116447. [PMID: 38714044 DOI: 10.1016/j.ejmech.2024.116447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 05/09/2024]
Abstract
Histone deacetylase 6 (HDAC6) is an emerging drug target to treat oncological and non-oncological conditions. Since highly selective HDAC6 inhibitors display limited anticancer activity when used as single agent, they usually require combination therapies with other chemotherapeutics. In this work, we synthesized a mini library of analogues of the preferential HDAC6 inhibitor HPOB in only two steps via an Ugi four-component reaction as the key step. Biochemical HDAC inhibition and cell viability assays led to the identification of 1g (highest antileukemic activity) and 2b (highest HDAC6 inhibition) as hit compounds. In subsequent combination screens, both 1g and especially 2b showed synergy with DNA methyltransferase inhibitor decitabine in acute myeloid leukemia (AML). Our findings highlight the potential of combining HDAC6 inhibitors with DNA methyltransferase inhibitors as a strategy to improve AML treatment outcomes.
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Affiliation(s)
- Maik Tretbar
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Julian Schliehe-Diecks
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Lukas von Bredow
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Kathrin Tan
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Martin Roatsch
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Jia-Wey Tu
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Marie Kemkes
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Melf Sönnichsen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Andrea Schöler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany.
| | - Finn K Hansen
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
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Khatun S, Bhagat RP, Amin SA, Jha T, Gayen S. Density functional theory (DFT) studies in HDAC-based chemotherapeutics: Current findings, case studies and future perspectives. Comput Biol Med 2024; 175:108468. [PMID: 38657469 DOI: 10.1016/j.compbiomed.2024.108468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
Density Functional Theory (DFT) is a quantum chemical computational method used to predict and analyze the electronic properties of atoms, molecules, and solids based on the density of electrons rather than wavefunctions. It provides insights into the structure, bonding, and behavior of different molecules, including those involved in the development of chemotherapeutic agents, such as histone deacetylase inhibitors (HDACis). HDACs are a wide group of metalloenzymes that facilitate the removal of acetyl groups from acetyl-lysine residues situated in the N-terminal tail of histones. Abnormal HDAC recruitment has been linked to several human diseases, especially cancer. Therefore, it has been recognized as a prospective target for accelerating the development of anticancer therapies. Researchers have studied HDACs and its inhibitors extensively using a combination of experimental methods and diverse in-silico approaches such as machine learning and quantitative structure-activity relationship (QSAR) methods, molecular docking, molecular dynamics, pharmacophore mapping, and more. In this context, DFT studies can make significant contribution by shedding light on the molecular properties, interactions, reaction pathways, transition states, reactivity and mechanisms involved in the development of HDACis. This review attempted to elucidate the scope in which DFT methodologies may be used to enhance our comprehension of the molecular aspects of HDAC inhibitors, aiding in the rational design and optimization of these compounds for therapeutic applications in cancer and other ailments. The insights gained can guide experimental efforts toward developing more potent and selective HDAC inhibitors.
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Affiliation(s)
- Samima Khatun
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Rinki Prasad Bhagat
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Sk Abdul Amin
- Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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18
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Yimiti M, Fei X, Yang H, Yang X, Li S, Tuoheniyazi H, Liu D, Ma J, Xie J, Zheng J, Song Z, Li Q, Xu D, Zhao Y, Gu Z. HDAC6 inhibitor promotes reactive oxygen species-meditated clearance of Staphylococcus aureus in macrophage. Clin Exp Pharmacol Physiol 2024; 51:e13866. [PMID: 38719209 DOI: 10.1111/1440-1681.13866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 05/30/2024]
Abstract
Staphylococcus aureus (S. aureus) pneumonia has become an increasingly important public health problem. Recent evidence suggests that epigenetic modifications are critical in the host immune defence against pathogen infection. In this study, we found that S. aureus infection induces the expression of histone deacetylase 6 (HDAC6) in a dose-dependent manner. Furthermore, by using a S. aureus pneumonia mouse model, we showed that the HDAC6 inhibitor, tubastatin A, demonstrates a protective effect in S. aureus pneumonia, decreasing the mortality and destruction of lung architecture, reducing the bacterial burden in the lungs and inhibiting inflammatory responses. Mechanistic studies in primary bone marrow-derived macrophages demonstrated that the HDAC6 inhibitors, tubastatin A and tubacin, reduced the intracellular bacterial load by promoting bacterial clearance rather than regulating phagocytosis. Finally, N-acetyl-L- cysteine, a widely used reactive oxygen species (ROS) scavenger, antagonized ROS production and significantly inhibited tubastatin A-induced S. aureus clearance. These findings demonstrate that HDAC6 inhibitors promote the bactericidal activity of macrophages by inducing ROS, an important host factor for S. aureus clearance and production. Our study identified HDAC6 as a suitable epigenetic modification target for preventing S. aureus infection, and tubastatin A as a useful compound in treating S. aureus pneumonia.
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Affiliation(s)
- Maimaitiaili Yimiti
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuefeng Fei
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Yang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaobao Yang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuhui Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huxidanmu Tuoheniyazi
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Danping Liu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junrui Ma
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jialing Xie
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Juanjuan Zheng
- Blood Transfusion Department, Qilu Hospital of Shandong University Dezhou Hospital, Dezhou, Shandong, China
| | - Zhen Song
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dakang Xu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanan Zhao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhidong Gu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, Ruijin-Hainan Hospital, Shanghai Jiao Tong University School of Medicine (Hainan Boao Research Hospital), Qionghai, Hainan, China
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19
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Cellupica E, Gaiassi A, Rocchio I, Rovelli G, Pomarico R, Sandrone G, Caprini G, Cordella P, Cukier C, Fossati G, Marchini M, Bebel A, Airoldi C, Palmioli A, Stevenazzi A, Steinkühler C, Vergani B. Mechanistic and Structural Insights on Difluoromethyl-1,3,4-oxadiazole Inhibitors of HDAC6. Int J Mol Sci 2024; 25:5885. [PMID: 38892072 PMCID: PMC11172862 DOI: 10.3390/ijms25115885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Histone deacetylase 6 (HDAC6) is increasingly recognized for its potential in targeted disease therapy. This study delves into the mechanistic and structural nuances of HDAC6 inhibition by difluoromethyl-1,3,4-oxadiazole (DFMO) derivatives, a class of non-hydroxamic inhibitors with remarkable selectivity and potency. Employing a combination of nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) kinetic experiments, comprehensive enzymatic characterizations, and X-ray crystallography, we dissect the intricate details of the DFMO-HDAC6 interaction dynamics. More specifically, we find that the chemical structure of a DMFO and the binding mode of its difluoroacetylhydrazide derivative are crucial in determining the predominant hydrolysis mechanism. Our findings provide additional insights into two different mechanisms of DFMO hydrolysis, thus contributing to a better understanding of the HDAC6 inhibition by oxadiazoles in disease modulation and therapeutic intervention.
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Affiliation(s)
- Edoardo Cellupica
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Aureliano Gaiassi
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Ilaria Rocchio
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Grazia Rovelli
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Roberta Pomarico
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Giovanni Sandrone
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Gianluca Caprini
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Paola Cordella
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Cyprian Cukier
- Department of Biochemistry, Selvita S.A., 30-394 Kraków, Poland; (C.C.); (A.B.)
| | - Gianluca Fossati
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Mattia Marchini
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Aleksandra Bebel
- Department of Biochemistry, Selvita S.A., 30-394 Kraków, Poland; (C.C.); (A.B.)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (C.A.); (A.P.)
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (C.A.); (A.P.)
| | - Andrea Stevenazzi
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Christian Steinkühler
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Barbara Vergani
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
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20
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Curcio A, Rocca R, Alcaro S, Artese A. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals (Basel) 2024; 17:620. [PMID: 38794190 PMCID: PMC11124352 DOI: 10.3390/ph17050620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) are crucial in gene transcription, removing acetyl groups from histones. They also influence the deacetylation of non-histone proteins, contributing to the regulation of various biological processes. Thus, HDACs play pivotal roles in various diseases, including cancer, neurodegenerative disorders, and inflammatory conditions, highlighting their potential as therapeutic targets. This paper reviews the structure and function of the four classes of human HDACs. While four HDAC inhibitors are currently available for treating hematological malignancies, numerous others are undergoing clinical trials. However, their non-selective toxicity necessitates ongoing research into safer and more efficient class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches, such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships, and structure-based virtual screening (molecular docking). Moreover, recent developments in the field of molecular dynamics simulations, combined with Poisson-Boltzmann/molecular mechanics generalized Born surface area techniques, have improved the prediction of ligand binding affinity. In this review, we delve into the ways in which these methods have contributed to designing and identifying HDAC inhibitors.
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Affiliation(s)
- Antonio Curcio
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
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21
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Abdulwahab HG, Mansour RES, Farghaly TA, El-Sehrawi HM. Discovery of novel benzimidazole derivatives as potent HDACs inhibitors against leukemia with (Thio)Hydantoin as zinc-binding moiety: Design, synthesis, enzyme inhibition, and cellular mechanistic study. Bioorg Chem 2024; 146:107284. [PMID: 38493640 DOI: 10.1016/j.bioorg.2024.107284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/02/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
Based on the well-established pharmacophoric features required for histone deacetylase (HDAC) inhibition, a novel series of easy-to-synthesize benzimidazole-linked (thio)hydantoin derivatives was designed and synthesized as HDAC6 inhibitors. All target compounds potently inhibited HDAC6 at nanomolar levels with compounds 2c, 2d, 4b and 4c (IC50s = 51.84-74.36 nM) being more potent than SAHA reference drug (IC50 = 91.73 nM). Additionally, the most potent derivatives were further assessed for their in vitro cytotoxic activity against two human leukemia cells. Hydantoin derivative 4c was equipotent/superior to SAHA against MOLT-4/CCRF-CEM leukemia cells, respectively and demonstrated safety profile better than that of SAHA against non-cancerous human cells. 4c was also screened against different HDAC isoforms. 4c was superior to SAHA against HDAC1. Cell-based assessment of 4c revealed a significant cell cycle arrest and apoptosis induction. Moreover, western blotting analysis showed increased levels of acetylated histone H3, histone H4 and α-tubulin in CCRF-CEM cells. Furthermore, docking study exposed the ability of title compounds to chelate Zn2+ located within HDAC6 active site. As well, in-silico evaluation of physicochemical properties showed that target compounds are promising candidates in terms of pharmacokinetic aspects.
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Affiliation(s)
- Hanan Gaber Abdulwahab
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt.
| | - Reda El-Sayed Mansour
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Thoraya A Farghaly
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Hend M El-Sehrawi
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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22
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Jia J, Jiao W, Wang G, Wu J, Huang Z, Zhang Y. Drugs/agents for the treatment of ischemic stroke: Advances and perspectives. Med Res Rev 2024; 44:975-1012. [PMID: 38126568 DOI: 10.1002/med.22009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
Ischemic stroke (IS) poses a significant threat to global human health and life. In recent decades, we have witnessed unprecedented progresses against IS, including thrombolysis, thrombectomy, and a few medicines that can assist in reopening the blocked brain vessels or serve as standalone treatments for patients who are not eligible for thrombolysis/thrombectomy therapies. However, the narrow time windows of thrombolysis/thrombectomy, coupled with the risk of hemorrhagic transformation, as well as the lack of highly effective and safe medications, continue to present big challenges in the acute treatment and long-term recovery of IS. In the past 3 years, several excellent articles have reviewed pathophysiology of IS and therapeutic medicines for the treatment of IS based on the pathophysiology. Regretfully, there is no comprehensive overview to summarize all categories of anti-IS drugs/agents designed and synthesized based on molecular mechanisms of IS pathophysiology. From medicinal chemistry view of point, this article reviews a multitude of anti-IS drugs/agents, including small molecule compounds, natural products, peptides, and others, which have been developed based on the molecular mechanism of IS pathophysiology, such as excitotoxicity, oxidative/nitrosative stresses, cell death pathways, and neuroinflammation, and so forth. In addition, several emerging medicines and strategies, including nanomedicines, stem cell therapy and noncoding RNAs, which recently appeared for the treatment of IS, are shortly introduced. Finally, the perspectives on the associated challenges and future directions of anti-IS drugs/agents are briefly provided to move the field forward.
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Affiliation(s)
- Jian Jia
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, China
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China
| | - Weijie Jiao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, China
| | - Guan Wang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China
| | - Jianbing Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, China
| | - Zhangjian Huang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, China
| | - Yihua Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing, China
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23
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Christianson DW. Chemical Versatility in Catalysis and Inhibition of the Class IIb Histone Deacetylases. Acc Chem Res 2024; 57:1135-1148. [PMID: 38530703 PMCID: PMC11021156 DOI: 10.1021/acs.accounts.3c00801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The zinc-dependent histone deacetylases (HDACs 1-11) belong to the arginase-deacetylase superfamily of proteins, members of which share a common α/β fold and catalytic metal binding site. While several HDACs play a role in epigenetic regulation by catalyzing acetyllysine hydrolysis in histone proteins, the biological activities of HDACs extend far beyond histones. HDACs also deacetylate nonhistone proteins in the nucleus as well as the cytosol to regulate myriad cellular processes. The substrate pool is even more diverse in that certain HDACs can hydrolyze other covalent modifications. For example, HDAC6 is also a lysine decrotonylase, and HDAC11 is a lysine-fatty acid deacylase. Surprisingly, HDAC10 is not a lysine deacetylase but instead is a polyamine deacetylase. Thus, the HDACs are biologically and chemically versatile catalysts as they regulate the function of diverse protein and nonprotein substrates throughout the cell.Owing to their critical regulatory functions, HDACs serve as prominent targets for drug design. At present, four HDAC inhibitors are FDA-approved for cancer chemotherapy. However, these inhibitors are active against multiple HDAC isozymes, and a lack of selectivity is thought to contribute to undesirable side effects. Current medicinal chemistry campaigns focus on the development of isozyme-selective inhibitors, and many such studies largely focus on HDAC6 and HDAC10. HDAC6 is a target for therapeutic intervention due to its cellular role as a tubulin deacetylase and tau deacetylase, and selective inhibitors are being studied in cancer chemotherapy and the treatment of peripheral neuropathy. Crystal structures of enzyme-inhibitor complexes reveal how various features of inhibitor design, such as zinc-coordinating groups, bifurcated capping groups, and aromatic fluorination patterns, contribute to affinity and isozyme selectivity. The polyamine deacetylase HDAC10 is also an emerging target for cancer chemotherapy. Crystal structures of intact substrates trapped in the HDAC10 active site reveal the molecular basis of strikingly narrow substrate specificity for N8-acetylspermidine hydrolysis. Active site features responsible for substrate specificity have been successfully exploited in the design of potent and selective inhibitors.In this Account, I review the structural chemistry and inhibition of HDACs, highlighting recent X-ray crystallographic and functional studies of HDAC6 and HDAC10 in my laboratory. These studies have yielded fascinating snapshots of catalysis as well as novel chemical transformations involving bound inhibitors. The zinc-bound water molecule in the HDAC active site is the catalytic nucleophile in the deacetylation reaction, but this activated water molecule can also react with inhibitor C═O or C═N groups to yield unanticipated reaction products that bind exceptionally tightly. Versatile active site chemistry unleashes the full inhibitory potential of such compounds, and X-ray crystallography allows us to view this chemistry in action.
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Affiliation(s)
- David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323, USA
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Pandaram A, Paul J, Wankhar W, Thakur A, Verma S, Vasudevan K, Wankhar D, Kammala AK, Sharma P, Jaganathan R, Iyaswamy A, Rajan R. Aspartame Causes Developmental Defects and Teratogenicity in Zebra Fish Embryo: Role of Impaired SIRT1/FOXO3a Axis in Neuron Cells. Biomedicines 2024; 12:855. [PMID: 38672209 PMCID: PMC11048232 DOI: 10.3390/biomedicines12040855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Aspartame, a widely used artificial sweetener, is present in many food products and beverages worldwide. It has been linked to potential neurotoxicity and developmental defects. However, its teratogenic effect on embryonic development and the underlying potential mechanisms need to be elucidated. We investigated the concentration- and time-dependent effects of aspartame on zebrafish development and teratogenicity. We focused on the role of sirtuin 1 (SIRT1) and Forkhead-box transcription factor (FOXO), two proteins that play key roles in neurodevelopment. It was found that aspartame exposure reduced the formation of larvae and the development of cartilage in zebrafish. It also delayed post-fertilization development by altering the head length and locomotor behavior of zebrafish. RNA-sequencing-based DEG analysis showed that SIRT1 and FOXO3a are involved in neurodevelopment. In silico and in vitro analyses showed that aspartame could target and reduce the expression of SIRT1 and FOXO3a proteins in neuron cells. Additionally, aspartame triggered the reduction of autophagy flux by inhibiting the nuclear translocation of SIRT1 in neuronal cells. The findings suggest that aspartame can cause developmental defects and teratogenicity in zebrafish embryos and reduce autophagy by impairing the SIRT1/FOXO3a axis in neuron cells.
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Affiliation(s)
- Athiram Pandaram
- Department of Physiology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai 600113, Tamil Nadu, India
| | - Jeyakumari Paul
- Department of Physiology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai 600113, Tamil Nadu, India
| | - Wankupar Wankhar
- Faculty of Paramedical Sciences, Assam down town University, Guwahati 781026, Assam, India
| | - Abhimanyu Thakur
- Pritzker School of Molecular Engineering, Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
| | - Sakshi Verma
- Department of Pharmacy, Usha Martin University, Ranchi 835103, Jharkhand, India
| | - Karthick Vasudevan
- Department of Biotechnology, REVA University, Bangalore 560064, Karnataka, India
| | - Dapkupar Wankhar
- Faculty of Paramedical Sciences, Assam down town University, Guwahati 781026, Assam, India
| | - Ananth Kumar Kammala
- Department of Obstetrics and Gynaecology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Priyanshu Sharma
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ravindran Jaganathan
- Preclinical Department, Faculty of Medicine, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh 30450, Perak, Malaysia
| | - Ashok Iyaswamy
- Mr. & Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India
| | - Ravindran Rajan
- Department of Physiology, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai 600113, Tamil Nadu, India
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Liu X, Cheng W, Yao P, Ren K, Wang Y, Sun Y, Hou X, Lu L, Chen X. Conserved serine phosphorylation regulates histone deacetylase activity in Arabidopsis and humans. PLANT PHYSIOLOGY 2024; 194:2017-2021. [PMID: 37966963 DOI: 10.1093/plphys/kiad587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/02/2023] [Indexed: 11/17/2023]
Abstract
Conserved serine phosphorylation regulates histone deacetylase activity in Arabidopsis and humans
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Affiliation(s)
- Xiaojing Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Weijia Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Peng Yao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Kexin Ren
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Yu Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Yingnan Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Xin Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Li Lu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiangsong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
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Sun C, Xie K, Yang L, Cai S, Wang M, Zhu Y, Tao B, Zhu Y. HDAC6 Enhances Endoglin Expression through Deacetylation of Transcription Factor SP1, Potentiating BMP9-Induced Angiogenesis. Cells 2024; 13:490. [PMID: 38534334 DOI: 10.3390/cells13060490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
Histone deacetylase 6 (HDAC6) plays a crucial role in the acetylation of non-histone proteins and is notably implicated in angiogenesis, though its underlying mechanisms were previously not fully understood. This study conducted transcriptomic and proteomic analyses on vascular endothelial cells with HDAC6 knockdown, identifying endoglin (ENG) as a key downstream protein regulated by HDAC6. This protein is vital for maintaining vascular integrity and plays a complex role in angiogenesis, particularly in its interaction with bone morphogenetic protein 9 (BMP9). In experiments using human umbilical vein endothelial cells (HUVECs), the pro-angiogenic effects of BMP9 were observed, which diminished following the knockdown of HDAC6 and ENG. Western blot analysis revealed that BMP9 treatment increased SMAD1/5/9 phosphorylation, a process hindered by HDAC6 knockdown, correlating with reduced ENG expression. Mechanistically, our study indicates that HDAC6 modulates ENG transcription by influencing promoter activity, leading to increased acetylation of transcription factor SP1 and consequently altering its transcriptional activity. Additionally, the study delves into the structural role of HDAC6, particularly its CD2 domain, in regulating SP1 acetylation and subsequently ENG expression. In conclusion, the present study underscores the critical function of HDAC6 in modulating SP1 acetylation and ENG expression, thereby significantly affecting BMP9-mediated angiogenesis. This finding highlights the potential of HDAC6 as a therapeutic target in angiogenesis-related processes.
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Affiliation(s)
- Chen Sun
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Avenida WaiLong, Taipa, Macau 999078, China
| | - Kuifang Xie
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Lejie Yang
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Shengyang Cai
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Mingjie Wang
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Yizhun Zhu
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Avenida WaiLong, Taipa, Macau 999078, China
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 200433, China
| | - Beibei Tao
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Yichun Zhu
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China
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Karati D, Mukherjee S, Roy S. Emerging therapeutic strategies in cancer therapy by HDAC inhibition as the chemotherapeutic potent and epigenetic regulator. Med Oncol 2024; 41:84. [PMID: 38438564 DOI: 10.1007/s12032-024-02303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/16/2024] [Indexed: 03/06/2024]
Abstract
In developing new cancer medications, attention has been focused on novel epigenetic medicines called histone deacetylase (HDAC) inhibitors. Our understanding of cancer behavior is being advanced by research on epigenetics, which also supplies new targets for improving the effectiveness of cancer therapy. Most recently published patents emphasize HDAC selective drugs and multitarget HDAC inhibitors. Though significant progress has been made in emerging HDAC selective antagonists, it is urgently necessary to find new HDAC blockers with novel zinc-binding analogues to avoid the undesirable pharmacological characteristics of hydroxamic acid. HDAC antagonists have lately been explored as a novel approach to treating various diseases, including cancer. The complicated terrain of HDAC inhibitor development is summarized in this article, starting with a discussion of the many HDAC isotypes and their involvement in cancer biology, followed by a discussion of the mechanisms of action of HDAC inhibitors, their current level of development, effect of miRNA, and their combination with immunotherapeutic.
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Affiliation(s)
- Dipanjan Karati
- Department of Pharmaceutical Technology, School of Pharmacy, Techno India University, Kolkata, 700091, India
| | - Swarupananda Mukherjee
- Department of Pharmaceutical Technology, NSHM Knowledge Campus, Kolkata, 124 B.L. Saha Road, Kolkata, West Bengal, 700053, India
| | - Souvik Roy
- Department of Pharmaceutical Technology, NSHM Knowledge Campus, Kolkata, 124 B.L. Saha Road, Kolkata, West Bengal, 700053, India.
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Mozzetta C, Sartorelli V, Steinkuhler C, Puri PL. HDAC inhibitors as pharmacological treatment for Duchenne muscular dystrophy: a discovery journey from bench to patients. Trends Mol Med 2024; 30:278-294. [PMID: 38408879 PMCID: PMC11095976 DOI: 10.1016/j.molmed.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/28/2024]
Abstract
Earlier evidence that targeting the balance between histone acetyltransferases (HATs) and deacetylases (HDACs), through exposure to HDAC inhibitors (HDACis), could enhance skeletal myogenesis, prompted interest in using HDACis to promote muscle regeneration. Further identification of constitutive HDAC activation in dystrophin-deficient muscles, caused by dysregulated nitric oxide (NO) signaling, provided the rationale for HDACi-based therapeutic interventions for Duchenne muscular dystrophy (DMD). In this review, we describe the molecular, preclinical, and clinical evidence supporting the efficacy of HDACis in countering disease progression by targeting pathogenic networks of gene expression in multiple muscle-resident cell types of patients with DMD. Given that givinostat is paving the way for HDACi-based interventions in DMD, next-generation HDACis with optimized therapeutic profiles and efficacy could be also explored for synergistic combinations with other therapeutic strategies.
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Affiliation(s)
- Chiara Mozzetta
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, Rome, Italy
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Pier Lorenzo Puri
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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29
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Uba AI, Hryb M, Singh M, Bui-Linh C, Tran A, Atienza J, Misbah S, Mou X, Wu C. Discovery of novel inhibitors of histone deacetylase 6: Structure-based virtual screening, molecular dynamics simulation, enzyme inhibition and cell viability assays. Life Sci 2024; 338:122395. [PMID: 38181853 DOI: 10.1016/j.lfs.2023.122395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/07/2024]
Abstract
Histone deacetylase 6 (HDAC6) contributes to cancer metastasis in several cancers, including triple-negative breast cancer (TNBC)-the most lethal form that lacks effective therapy. Although several efforts have been invested to develop selective HDAC6 inhibitors, none have been approved by the FDA. Toward this goal, existing computational studies used smaller compound libraries and shorter MD simulations. Here, we conducted a structure-based virtual screening of ZINC "Druglike" library containing 17,900,742 compounds using a Glide virtual screening protocol comprising various filters with increasing accuracy. The top 20 hits were subjected to molecular dynamics simulation, MM-GBSA binding energy calculations, and further ADMET prediction. Furthermore, enzyme inhibition assay and cell viability assay were performed on six available compounds from the identified hits. C4 (ZINC000077541942) with a good profile of predicted drug properties was found to inhibit HDAC6 (IC50: 4.7 ± 11.6 μM) with comparative affinity to that of the known HDAC6 selective inhibitor Tubacin (TA) in our experiments. C4 also demonstrated cytotoxic effects against triple-negative breast cancer (TNBC) cell line MDA-MB-231 with EC50 of 40.6 ± 12.7 μM comparable to that of TA (2-20 μM). Therefore, this compound, with pharmacophore features comprising a non-hydroxamic acid zinc-binding group, heteroaromatic linker, and cap group, is proposed as a novel HDAC6 inhibitor.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Complex Systems Division, Beijing Computational Science Research Center, Beijing 100193, China
| | - Mariya Hryb
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Mursalin Singh
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Candice Bui-Linh
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Annie Tran
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Jiancarlo Atienza
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Sarah Misbah
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA
| | - Xiaoyang Mou
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA.
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, USA.
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30
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Kraft FB, Enns J, Honin I, Engelhardt J, Schöler A, Smith ST, Meiler J, Schäker-Hübner L, Weindl G, Hansen FK. Groebke Blackburn Bienaymé-mediated multi-component synthesis of selective HDAC6 inhibitors with anti-inflammatory properties. Bioorg Chem 2024; 143:107072. [PMID: 38185013 DOI: 10.1016/j.bioorg.2023.107072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/09/2024]
Abstract
Histone deacetylases (HDACs) are a class of enzymes that cleave acyl groups from lysine residues of histone and non-histone proteins. There are 18 human HDAC isoforms with different cellular targets and functions. Among them, HDAC6 was found to be overexpressed in different types of cancer. However, when used in monotherapy, HDAC6 inhibition by selective inhibitors fails to show pronounced anti-cancer effects. The HDAC6 enzyme also addresses non-histone proteins like α-tubulin and cortactin, making it important for cell migration and angiogenesis. Recently, the NLRP3 inflammasome was identified as an important regulator of inflammation and immune responses and, importantly, HDAC6 is critically involved the activation of the inflammasome. We herein report the design, synthesis and biological evaluation of a library of selective HDAC6 inhibitors. Starting from the previously published crystal structure of MAIP-032 in complex with CD2 of zHDAC6, we performed docking studies to evaluate additional possible interactions of the cap group with the L1-loop pocket. Based on the results we synthesized 13 novel HDAC6 inhibitors via the Groebke-Blackburn-Bienaymé three component reaction as the key step. Compounds 8k (HDAC1 IC50: 5.87 μM; HDAC6 IC50: 0.024 μM; selectivity factor (SF1/6): 245) and 8m (HDAC1 IC50: 3.07 μM; HDAC6 IC50: 0.026 μM; SF1/6: 118) emerged as the most potent and selective inhibitors of HDAC6 and outperformed the lead structure MAIP-032 (HDAC1 IC50: 2.20 μM; HDAC6 IC50: 0.058 μM; SF1/6: 38) both in terms of inhibitory potency and selectivity. Subsequent immunoblot analysis confirmed the high selectivity of 8k and 8m for HDAC6 in a cellular environment. While neither 8k and 8m nor the selectivity HDAC6 inhibitor tubastatin A showed antiproliferative effects in the U-87 MG glioblastoma cell line, compound 8m attenuated cell migration significantly in wound healing assays in U-87 MG cells. Moreover, in macrophages compounds 8k and 8m demonstrated significant inhibition of LPS-induced IL1B mRNA expression and TNF release. These findings suggest that our imidazo[1,2-a]pyridine-capped HDAC6 inhibitors may serve as promising candidates for the development of drugs to effectively treat NLRP3 inflammasome-driven inflammatory diseases.
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Affiliation(s)
- Fabian B Kraft
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Jana Enns
- Department of Pharmacology and Toxicology, Pharmaceutical Institute, University of Bonn, Gerhard-Domagk-Str.3, 53121 Bonn, Germany
| | - Irina Honin
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Jonas Engelhardt
- Department of Pharmacology and Toxicology, Pharmaceutical Institute, University of Bonn, Gerhard-Domagk-Str.3, 53121 Bonn, Germany
| | - Andrea Schöler
- Institute for Drug Discovery, Medicinal Faculty, University Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Shannon T Smith
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Jens Meiler
- Institute for Drug Discovery, Medicinal Faculty, University Leipzig, Brüderstraße 34, 04103 Leipzig, Germany; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Linda Schäker-Hübner
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Günther Weindl
- Department of Pharmacology and Toxicology, Pharmaceutical Institute, University of Bonn, Gerhard-Domagk-Str.3, 53121 Bonn, Germany
| | - Finn K Hansen
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany.
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Waitman KB, de Almeida LC, Primi MC, Carlos JAEG, Ruiz C, Kronenberger T, Laufer S, Goettert MI, Poso A, Vassiliades SV, de Souza VAM, Toledo MFZJ, Hassimotto NMA, Cameron MD, Bannister TD, Costa-Lotufo LV, Machado-Neto JA, Tavares MT, Parise-Filho R. HDAC specificity and kinase off-targeting by purine-benzohydroxamate anti-hematological tumor agents. Eur J Med Chem 2024; 263:115935. [PMID: 37989057 DOI: 10.1016/j.ejmech.2023.115935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
A series of hybrid inhibitors, combining pharmacophores of known kinase inhibitors bearing anilino-purines (ruxolitinib, ibrutinib) and benzohydroxamate HDAC inhibitors (nexturastat A), were generated in the present study. The compounds have been synthesized and tested against solid and hematological tumor cell lines. Compounds 4d-f were the most promising in cytotoxicity assays (IC50 ≤ 50 nM) vs. hematological cells and displayed moderate activity in solid tumor models (EC50 = 9.3-21.7 μM). Compound 4d potently inhibited multiple kinase targets of interest for anticancer effects, including JAK2, JAK3, HDAC1, and HDAC6. Molecular dynamics simulations showed that 4d has stable interactions with HDAC and members of the JAK family, with differences in the hinge binding energy conferring selectivity for JAK3 and JAK2 over JAK1. The kinase inhibition profile of compounds 4d-f allows selective cytotoxicity, with minimal effects on non-tumorigenic cells. Moreover, these compounds have favorable pharmacokinetic profiles, with high stability in human liver microsomes (e.g., see t1/2: >120 min for 4f), low intrinsic clearance, and lack of significant inhibition of four major CYP450 isoforms.
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Affiliation(s)
- Karoline B Waitman
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Larissa C de Almeida
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marina C Primi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, United States
| | - Jorge A E G Carlos
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudia Ruiz
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, United States
| | - Thales Kronenberger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland; Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), 72076, Tübingen, Germany
| | - Stefan Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany
| | - Marcia Ines Goettert
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland; Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), 72076, Tübingen, Germany
| | - Sandra V Vassiliades
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vinícius A M de Souza
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mônica F Z J Toledo
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Neuza M A Hassimotto
- Food Research Center-(FoRC-CEPID) and Department of Food Science and Nutrition, Faculty of Pharmaceutical Science, University of São Paulo, São Paulo, SP, Brazil
| | - Michael D Cameron
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, United States
| | - Thomas D Bannister
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, United States
| | - Letícia V Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - João A Machado-Neto
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maurício T Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, United States.
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
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Vuletić A, Mirjačić Martinović K, Spasić J. Role of Histone Deacetylase 6 and Histone Deacetylase 6 Inhibition in Colorectal Cancer. Pharmaceutics 2023; 16:54. [PMID: 38258065 PMCID: PMC10818982 DOI: 10.3390/pharmaceutics16010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Histone deacetylase 6 (HDAC6), by deacetylation of multiple substrates and association with interacting proteins, regulates many physiological processes that are involved in cancer development and invasiveness such as cell proliferation, apoptosis, motility, epithelial to mesenchymal transition, and angiogenesis. Due to its ability to remove misfolded proteins, induce autophagy, and regulate unfolded protein response, HDAC6 plays a protective role in responses to stress and enables tumor cell survival. The scope of this review is to discuss the roles of HDCA6 and its implications for the therapy of colorectal cancer (CRC). As HDAC6 is overexpressed in CRC, correlates with poor disease prognosis, and is not essential for normal mammalian development, it represents a good therapeutic target. Selective inhibition of HDAC6 impairs growth and progression without inducing major adverse events in experimental animals. In CRC, HDAC6 inhibitors have shown the potential to reduce tumor progression and enhance the therapeutic effect of other drugs. As HDAC6 is involved in the regulation of immune responses, HDAC6 inhibitors have shown the potential to improve antitumor immunity by increasing the immunogenicity of tumor cells, augmenting immune cell activity, and alleviating immunosuppression in the tumor microenvironment. Therefore, HDAC6 inhibitors may represent promising candidates to improve the effect of and overcome resistance to immunotherapy.
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Affiliation(s)
- Ana Vuletić
- Department of Experimental Oncology, Institute of Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Katarina Mirjačić Martinović
- Department of Experimental Oncology, Institute of Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Jelena Spasić
- Clinic for Medical Oncology, Institute of Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
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33
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Artcibasova A, Wang L, Anchisi S, Yamauchi Y, Schmolke M, Matthias P, Stelling J. A quantitative model for virus uncoating predicts influenza A infectivity. Cell Rep 2023; 42:113558. [PMID: 38103200 DOI: 10.1016/j.celrep.2023.113558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/13/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
For virus infection of new host cells, the disassembly of the protective outer protein shell (capsid) is a critical step, but the mechanisms and host-virus interactions underlying the dynamic, active, and regulated uncoating process are largely unknown. Here, we develop an experimentally supported, multiscale kinetics model that elucidates mechanisms of influenza A virus (IAV) uncoating in cells. Biophysical modeling demonstrates that interactions between capsid M1 proteins, host histone deacetylase 6 (HDAC6), and molecular motors can physically break the capsid in a tug-of-war mechanism. Biochemical analysis and biochemical-biophysical modeling identify unanchored ubiquitin chains as essential and allow robust prediction of uncoating efficiency in cells. Remarkably, the different infectivity of two clinical strains can be ascribed to a single amino acid variation in M1 that affects binding to HDAC6. By identifying crucial modules of viral infection kinetics, the mechanisms and models presented here could help formulate novel strategies for broad-range antiviral treatment.
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Affiliation(s)
- Alina Artcibasova
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland
| | - Longlong Wang
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland
| | - Stephanie Anchisi
- Department of Microbiology and Molecular Medicine and Geneva Center of Inflammation Research, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Yohei Yamauchi
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Mirco Schmolke
- Department of Microbiology and Molecular Medicine and Geneva Center of Inflammation Research, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland.
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland.
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34
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Feller F, Hansen FK. Targeted Protein Degradation of Histone Deacetylases by Hydrophobically Tagged Inhibitors. ACS Med Chem Lett 2023; 14:1863-1868. [PMID: 38116436 PMCID: PMC10726458 DOI: 10.1021/acsmedchemlett.3c00468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
There is a growing interest in alternative strategies for targeted protein degradation. In this work, we present the development of histone deacetylase (HDAC) degraders based on hydrophobic tagging technology. To this end, a library of hydrophobically tagged HDAC inhibitors was synthesized via efficient solid-phase protocols utilizing pre-loaded resins. The subsequent biological evaluation led to the identification of our best degrader, 1a, which significantly decreased HDAC1 levels in MM.1S multiple myeloma cells.
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Affiliation(s)
- Felix Feller
- Department of Pharmaceutical
and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Finn K. Hansen
- Department of Pharmaceutical
and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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35
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Duda J, Thomas SN. Interactions of Histone Deacetylase 6 with DNA Damage Repair Factors Strengthen its Utility as a Combination Drug Target in High-Grade Serous Ovarian Cancer. ACS Pharmacol Transl Sci 2023; 6:1924-1933. [PMID: 38107255 PMCID: PMC10723650 DOI: 10.1021/acsptsci.3c00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 12/19/2023]
Abstract
High-grade serous ovarian cancer (HGSOC) is the deadliest gynecologic malignancy in women. The low survival rate is largely due to drug resistance. Approximately 80% of patients who initially respond to treatment relapse and become drug-resistant. The lack of effective second-line therapeutics remains a substantial challenge for BRCA-1/2 wild-type HGSOC patients. Histone Deacetylases (HDACs) are promising targets in HGSOC treatment; however, the mechanism and efficacy of HDAC inhibitors are understudied in HGSOC. In order to consider HDACs as a treatment target, an improved understanding of their function within HGSOC is required. This includes elucidating HDAC6-specific protein-protein interactions. In this study, we carried out substrate trapping followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to elucidate HDAC6 catalytic domain (CD)-specific interactors in the context of BRCA-1/2 wild-type HGSOC. Overall, this study identified new HDAC6 substrates that may be unique to HGSOC. The HDAC6-CD1 mutant condition contained the largest number of significant proteins compared to the CD2 mutant and the CD1/2 mutant conditions, suggesting the HDAC6-CD1 domain has catalytic activity that is independent of CD2. Among the identified substrates were proteins involved in DNA damage repair including PARP proteins. These findings further justify the use of HDAC inhibitors as a combination treatment with platinum chemotherapy agents and PARP inhibitors in HGSOC.
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Affiliation(s)
- Jolene
M. Duda
- Department
of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Stefani N. Thomas
- Department
of Laboratory Medicine and Pathology, University
of Minnesota, Minneapolis, Minnesota 55455, United States
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36
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Peng X, Yu Z, Surineni G, Deng B, Zhang M, Li C, Sun Z, Pan W, Liu Y, Liu S, Yu B, Chen J. Discovery of novel benzohydroxamate-based histone deacetylase 6 (HDAC6) inhibitors with the ability to potentiate anti-PD-L1 immunotherapy in melanoma. J Enzyme Inhib Med Chem 2023; 38:2201408. [PMID: 37096557 PMCID: PMC10132229 DOI: 10.1080/14756366.2023.2201408] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/26/2023] Open
Abstract
In this study, a novel series of histone deacetylases 6 (HDAC6) inhibitors containing polycyclic aromatic rings were discovered and evaluated for their pharmacological activities. The most potent compound 10c exhibited high HDAC6 inhibitory activity (IC50 = 261 nM) and excellent HDAC6 selectivity (SI = 109 for HDAC6 over HDAC3). 10c also showed decent antiproliferative activity in vitro with IC50 of 7.37-21.84 μM against four cancer cell lines, comparable to that of tubastatin A (average IC50 = 6.10 μM). Further mechanism studies revealed that 10c efficiently induced apoptosis and S-phase arrest in B16-F10 cells. In addition, 10c markedly increased the expression of acetylated-α-tubulin both in vitro and in vivo, without affecting the levels of acetylated-H3 (marker of HDAC1 inhibition). Furthermore, 10c (80 mg/kg) exhibited moderate antitumor efficacy in a melanoma tumour model with a tumour growth inhibition (TGI) of 32.9%, comparable to that (TGI = 31.3%) of tubastatin A. Importantly, the combination of 10c with NP19 (a small molecule PD-L1 inhibitor discovered by us before) decreased tumour burden substantially (TGI% = 60.1%) as compared to monotherapy groups. Moreover, the combination of 10c with NP19 enhanced the anti-tumour immune response, mediated by a decrease of PD-L1 expression levels and increased infiltration of anti-tumour CD8+ T cells in tumour tissues. Collectively, 10c represents a novel HDAC6 inhibitor deserving further investigation as a potential anti-cancer agent.
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Affiliation(s)
- Xiaopeng Peng
- College of Pharmacy, Gannan Medical University, Ganzhou, China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
| | - Ziwen Yu
- College of Pharmacy, Gannan Medical University, Ganzhou, China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
| | - Goverdhan Surineni
- College of Pharmacy, Gannan Medical University, Ganzhou, China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
| | - Bulian Deng
- College of Pharmacy, Gannan Medical University, Ganzhou, China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
| | - Meizhu Zhang
- College of Pharmacy, Gannan Medical University, Ganzhou, China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
| | - Chuan Li
- College of Pharmacy, Gannan Medical University, Ganzhou, China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
| | - Zhiqiang Sun
- College of Pharmacy, Gannan Medical University, Ganzhou, China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
| | - Wanyi Pan
- College of Pharmacy, Gannan Medical University, Ganzhou, China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
| | - Yao Liu
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Shenglan Liu
- College of Pharmacy, Gannan Medical University, Ganzhou, China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianjun Chen
- College of Pharmacy, Gannan Medical University, Ganzhou, China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
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37
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Pichlak M, Sobierajski T, Błażewska KM, Gendaszewska-Darmach E. Targeting reversible post-translational modifications with PROTACs: a focus on enzymes modifying protein lysine and arginine residues. J Enzyme Inhib Med Chem 2023; 38:2254012. [PMID: 37667522 PMCID: PMC10481767 DOI: 10.1080/14756366.2023.2254012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/17/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023] Open
Abstract
PROTACs represent an emerging field in medicinal chemistry, which has already led to the development of compounds that reached clinical studies. Posttranslational modifications contribute to the complexity of proteomes, with 2846 disease-associated sites. PROTAC field is very advanced in targeting kinases, while its use for enzymes mediating posttranslational modifications of the basic amino acid residues, started to be developed recently. Therefore, we bring together this less popular class of PROTACs, targeting lysine acetyltransferases/deacetylases, lysine and arginine methyltransferases, ADP-ribosyltransferases, E3 ligases, and ubiquitin-specific proteases. We put special emphasis on structural aspects of PROTAC elements to facilitate the lengthy experimental endeavours directed towards developing PROTACs. We will cover the period from the inception of the field, 2017, to April 2023.
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Affiliation(s)
- Marta Pichlak
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland
| | - Tomasz Sobierajski
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
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38
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Papa A, Cursaro I, Pozzetti L, Contri C, Cappello M, Pasquini S, Carullo G, Ramunno A, Gemma S, Varani K, Butini S, Campiani G, Vincenzi F. Pioneering first-in-class FAAH-HDAC inhibitors as potential multitarget neuroprotective agents. Arch Pharm (Weinheim) 2023; 356:e2300410. [PMID: 37750286 DOI: 10.1002/ardp.202300410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/27/2023]
Abstract
Aiming to simultaneously modulate the endocannabinoid system (ECS) functions and the epigenetic machinery, we selected the fatty acid amide hydrolase (FAAH) and histone deacetylase (HDAC) enzymes as desired targets to develop potential neuroprotective multitarget-directed ligands (MTDLs), expecting to achieve an additive or synergistic therapeutic effect in oxidative stress-related conditions. We herein report the design, synthesis, and biological evaluation of the first-in-class FAAH-HDAC multitarget inhibitors. A pharmacophore merging strategy was applied, yielding 1-phenylpyrrole-based compounds 4a-j. The best-performing compounds (4c, 4f, and 4h) were tested for their neuroprotective properties in oxidative stress models, employing 1321N1 human astrocytoma cells and SHSY5 human neuronal cells. In our preliminary studies, compound 4h stood out, showing a balanced nanomolar inhibitory activity against the selected targets and outperforming the standard antioxidant N-acetylcysteine in vitro. Together with 4f, 4h was also able to protect 1321N1 cells from tert-butyl hydroperoxide or glutamate insult. Our study may provide the basis for the development of novel MTDLs targeting the ECS and epigenetic enzymes.
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Affiliation(s)
- Alessandro Papa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Ilaria Cursaro
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Luca Pozzetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Chiara Contri
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Martina Cappello
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Silvia Pasquini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Gabriele Carullo
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Anna Ramunno
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Katia Varani
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Fabrizio Vincenzi
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
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39
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Baselious F, Robaa D, Sippl W. Utilization of AlphaFold models for drug discovery: Feasibility and challenges. Histone deacetylase 11 as a case study. Comput Biol Med 2023; 167:107700. [PMID: 37972533 DOI: 10.1016/j.compbiomed.2023.107700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Histone deacetylase 11 (HDAC11), an enzyme that cleaves acyl groups from acylated lysine residues, is the sole member of class IV of HDAC family with no reported crystal structure so far. The catalytic domain of HDAC11 shares low sequence identity with other HDAC isoforms which complicates the conventional template-based homology modeling. AlphaFold is a neural network machine learning approach for predicting the 3D structures of proteins with atomic accuracy even in absence of similar structures. However, the structures predicted by AlphaFold are missing small molecules as ligands and cofactors. In our study, we first optimized the HDAC11 AlphaFold model by adding the catalytic zinc ion followed by assessment of the usability of the model by docking of the selective inhibitor FT895. Minimization of the optimized model in presence of transplanted inhibitors, which have been described as HDAC11 inhibitors, was performed. Four complexes were generated and proved to be stable using three replicas of 50 ns MD simulations and were successfully utilized for docking of the selective inhibitors FT895, MIR002 and SIS17. For SIS17, The most reasonable pose was selected based on structural comparison between HDAC6, HDAC8 and the HDAC11 optimized AlphaFold model. The manually optimized HDAC11 model is thus able to explain the binding behavior of known HDAC11 inhibitors and can be used for further structure-based optimization.
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Affiliation(s)
- Fady Baselious
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
| | - Dina Robaa
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany.
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40
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Moi D, Bonanni D, Belluti S, Linciano P, Citarella A, Franchini S, Sorbi C, Imbriano C, Pinzi L, Rastelli G. Discovery of potent pyrrolo-pyrimidine and purine HDAC inhibitors for the treatment of advanced prostate cancer. Eur J Med Chem 2023; 260:115730. [PMID: 37633202 DOI: 10.1016/j.ejmech.2023.115730] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023]
Abstract
The development of drugs for the treatment of advanced prostate cancer (PCA) remains a challenging task. In this study we have designed, synthesized and tested twenty-nine novel HDAC inhibitors based on three different zinc binding groups (trifluoromethyloxadiazole, hydroxamic acid, and 2-mercaptoacetamide). These warheads were conveniently tethered to variously substituted phenyl linkers and decorated with differently substituted pyrrolo-pyrimidine and purine cap groups. Remarkably, most of the compounds showed nanomolar inhibitory activity against HDAC6. To provide structural insights into the Structure-Activity Relationships (SAR) of the investigated compounds, docking of representative inhibitors and molecular dynamics of HDAC6-inhibitor complexes were performed. Compounds of the trifluoromethyloxadiazole and hydroxamic acid series exhibited promising anti-proliferative activities, HDAC6 targeting in PCA cells, and in vitro tumor selectivity. Representative compounds of the two series were tested for solubility, cell permeability and metabolic stability, demonstrating favorable in vitro drug-like properties. The more interesting compounds were subjected to migration assays, which revealed that compound 13 and, to a lesser extent, compound 15 inhibited the invasive behaviour of androgen-sensitive and -insensitive advanced prostate cancer cells. Compound 13 was profiled against all HDACs and found to inhibit all members of class II HDACs (except for HDAC10) and to be selective with respect to class I and class IV HDACs. Overall, compound 13 combines potent inhibitory activity and class II selectivity with favorable drug-like properties, an excellent anti-proliferative activity and marked anti-migration properties on PCA cells, making it an excellent lead candidate for further optimization.
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Affiliation(s)
- Davide Moi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Davide Bonanni
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Andrea Citarella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Silvia Franchini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Claudia Sorbi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
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41
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Hobson AD. Antibody drug conjugates beyond cytotoxic payloads. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:1-59. [PMID: 37981349 DOI: 10.1016/bs.pmch.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
For many years, antibody drug conjugates (ADC) have teased with the promise of targeted payload delivery to diseased cells, embracing the targeting of the antibody to which a cytotoxic payload is conjugated. During the past decade this promise has started to be realised with the approval of more than a dozen ADCs for the treatment of various cancers. Of these ADCs, brentuximab vedotin really laid the foundations of a template for a successful ADC with lysosomal payload release from a cleavable dipeptide linker, measured DAR by conjugation to the Cys-Cys interchain bonds of the antibody and a cytotoxic payload. Using this ADC design model oncology has now expanded their repertoire of payloads to include non-cytotoxic compounds. These new payload classes have their origins in prior medicinal chemistry programmes aiming to design selective oral small molecule drugs. While this may not have been achieved, the resulting compounds provide excellent starting points for ADC programmes with some compounds amenable to immediate linker attachment while for others extensive SAR and structural information offer invaluable design insights. Many of these new oncology payload classes are of interest to other therapeutic areas facilitating rapid access to drug-linkers for exploration as non-oncology ADCs. Other therapeutic areas have also pursued unique payload classes with glucocorticoid receptor modulators (GRM) being the most clinically advanced in immunology. Here, ADC payloads come full circle, as oncology is now investigating GRM payloads for the treatment of cancer. This chapter aims to cover all these new ADC approaches while describing the medicinal chemistry origins of the new non-cytotoxic payloads.
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Affiliation(s)
- Adrian D Hobson
- Small Molecule Therapeutics & Platform Technologies, AbbVie Bioresearch Center, Worcester, MA, United States.
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42
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Sinatra L, Vogelmann A, Friedrich F, Tararina MA, Neuwirt E, Colcerasa A, König P, Toy L, Yesiloglu TZ, Hilscher S, Gaitzsch L, Papenkordt N, Zhai S, Zhang L, Romier C, Einsle O, Sippl W, Schutkowski M, Gross O, Bendas G, Christianson DW, Hansen FK, Jung M, Schiedel M. Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation. J Med Chem 2023; 66:14787-14814. [PMID: 37902787 PMCID: PMC10641818 DOI: 10.1021/acs.jmedchem.3c01385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/31/2023]
Abstract
Dysregulation of both tubulin deacetylases sirtuin 2 (Sirt2) and the histone deacetylase 6 (HDAC6) has been associated with the pathogenesis of cancer and neurodegeneration, thus making these two enzymes promising targets for pharmaceutical intervention. Herein, we report the design, synthesis, and biological characterization of the first-in-class dual Sirt2/HDAC6 inhibitors as molecular tools for dual inhibition of tubulin deacetylation. Using biochemical in vitro assays and cell-based methods for target engagement, we identified Mz325 (33) as a potent and selective inhibitor of both target enzymes. Inhibition of both targets was further confirmed by X-ray crystal structures of Sirt2 and HDAC6 in complex with building blocks of 33. In ovarian cancer cells, 33 evoked enhanced effects on cell viability compared to single or combination treatment with the unconjugated Sirt2 and HDAC6 inhibitors. Thus, our dual Sirt2/HDAC6 inhibitors are important new tools to study the consequences and the therapeutic potential of dual inhibition of tubulin deacetylation.
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Affiliation(s)
- Laura Sinatra
- Institute
for Drug Discovery, Medical Faculty, Leipzig
University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Anja Vogelmann
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Florian Friedrich
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Margarita A. Tararina
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Emilia Neuwirt
- Institute
of Neuropathology, Medical Center−University of Freiburg, Faculty
of Medicine, University of Freiburg, Breisacherstraße 64, 79106 Freiburg, Germany
- CIBSS−Centre
for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
| | - Arianna Colcerasa
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Philipp König
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Lara Toy
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Talha Z. Yesiloglu
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 2-4, 06120 Halle (Saale), Germany
| | - Sebastian Hilscher
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 2-4, 06120 Halle (Saale), Germany
- Department
of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry
and Biotechnology, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Lena Gaitzsch
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Niklas Papenkordt
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Shiyang Zhai
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Lin Zhang
- Institute
of Biochemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Christophe Romier
- Institut
de Génétique et de Biologie Moléculaire et Cellulaire
(IGBMC), Université de Strasbourg,
CNRS UMR 7104, Inserm UMR-S 1258, 1 rue Laurent Fries, F-67400 Illkirch, France
| | - Oliver Einsle
- Institute
of Biochemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Wolfgang Sippl
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 2-4, 06120 Halle (Saale), Germany
| | - Mike Schutkowski
- Department
of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry
and Biotechnology, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Olaf Gross
- Institute
of Neuropathology, Medical Center−University of Freiburg, Faculty
of Medicine, University of Freiburg, Breisacherstraße 64, 79106 Freiburg, Germany
- CIBSS−Centre
for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Center
for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Breisacherstraße 64, 79106 Freiburg, Germany
| | - Gerd Bendas
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - David W. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Finn K. Hansen
- Institute
for Drug Discovery, Medical Faculty, Leipzig
University, Brüderstraße 34, 04103 Leipzig, Germany
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Manfred Jung
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Matthias Schiedel
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
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43
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Beljkas M, Ilic A, Cebzan A, Radovic B, Djokovic N, Ruzic D, Nikolic K, Oljacic S. Targeting Histone Deacetylases 6 in Dual-Target Therapy of Cancer. Pharmaceutics 2023; 15:2581. [PMID: 38004560 PMCID: PMC10674519 DOI: 10.3390/pharmaceutics15112581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Histone deacetylases (HDACs) are the major regulators of the balance of acetylation of histone and non-histone proteins. In contrast to other HDAC isoforms, HDAC6 is mainly involved in maintaining the acetylation balance of many non-histone proteins. Therefore, the overexpression of HDAC6 is associated with tumorigenesis, invasion, migration, survival, apoptosis and growth of various malignancies. As a result, HDAC6 is considered a promising target for cancer treatment. However, none of selective HDAC6 inhibitors are in clinical use, mainly because of the low efficacy and high concentrations used to show anticancer properties, which may lead to off-target effects. Therefore, HDAC6 inhibitors with dual-target capabilities represent a new trend in cancer treatment, aiming to overcome the above problems. In this review, we summarize the advances in tumor treatment with dual-target HDAC6 inhibitors.
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Affiliation(s)
| | | | | | | | | | | | - Katarina Nikolic
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (M.B.); (A.I.); (A.C.); (B.R.); (N.D.); (D.R.)
| | - Slavica Oljacic
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (M.B.); (A.I.); (A.C.); (B.R.); (N.D.); (D.R.)
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44
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Barbaraci C, di Giacomo V, Maruca A, Patamia V, Rocca R, Dichiara M, Di Rienzo A, Cacciatore I, Cataldi A, Balaha M, Rapino M, Zagni C, Zampieri D, Pasquinucci L, Parenti C, Amata E, Rescifina A, Alcaro S, Marrazzo A. Discovery of first novel sigma/HDACi dual-ligands with a potent in vitro antiproliferative activity. Bioorg Chem 2023; 140:106794. [PMID: 37659146 DOI: 10.1016/j.bioorg.2023.106794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 09/04/2023]
Abstract
Designing and discovering compounds for dual-target inhibitors is challenging to synthesize new, safer, and more efficient drugs than single-target drugs, especially to treat multifactorial diseases such as cancer. The simultaneous regulation of multiple targets might represent an alternative synthetic approach to optimize patient compliance and tolerance, minimizing the risk of target-based drug resistance due to the modulation of a few targets. To this end, we conceived for the first time the design and synthesis of dual-ligands σR/HDACi to evaluate possible employment as innovative candidates to address this complex disease. Among all synthesized compounds screened for several tumoral cell lines, compound 6 (Kiσ1R = 38 ± 3.7; Kiσ2R = 2917 ± 769 and HDACs IC50 = 0.59 µM) is the most promising candidate as an antiproliferative agent with an IC50 of 0.9 µM on the HCT116 cell line and no significant toxicity to normal cells. Studies of molecular docking, which confirmed the affinity over σ1R and a pan-HDACs inhibitory behavior, support a possible balanced affinity and activity between both targets.
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Affiliation(s)
- Carla Barbaraci
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Viviana di Giacomo
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Annalisa Maruca
- Net4science academic spinoff srl, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Vincenzo Patamia
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Roberta Rocca
- Net4science academic spinoff srl, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Maria Dichiara
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Annalisa Di Rienzo
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Ivana Cacciatore
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Amelia Cataldi
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Marwa Balaha
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafr El Sheikh 33516, Egypt
| | - Monica Rapino
- Genetic Molecular Institute of CNR, Unit of Chieti, "G. d' Annunzio" University, Via dei Vestini 31, 66100 Chieti-Pescara, Italy
| | - Chiara Zagni
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Daniele Zampieri
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Lorella Pasquinucci
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Carmela Parenti
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Emanuele Amata
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Stefano Alcaro
- Net4science academic spinoff srl, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy; Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy.
| | - Agostino Marrazzo
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
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Wang B, Liu Y, Zhang L, Wang Y, Li Z, Chen X. Design, Synthesis, and Antiproliferative Activity of Selective Histone Deacetylases 6 Inhibitors Containing a Tetrahydropyridopyrimidine Scaffold. Molecules 2023; 28:7323. [PMID: 37959743 PMCID: PMC10648541 DOI: 10.3390/molecules28217323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The development of selective histone deacetylase 6 inhibitors (sHDAC6is) is being recognized as a therapeutic approach for cancers. In this paper, we designed a series of novel tetrahydropyridopyrimidine derivatives as sHDAC6 inhibitors. The most potent compound, 8-(2, 4-bis(3-methoxyphenyl)-5, 8-dihydropyrido [3, 4-d]pyrimidin-7(6H)-yl)-N-hydroxy-8-oxooctanamide (8f), inhibited HDAC6 with IC50 of 6.4 nM, and showed > 48-fold selectivity over other subtypes. In Western blot assay, 8f elevated the levels of acetylated α-tubulin in a dose-dependent manner. In vitro, 8f inhibited RPMI-8226, HL60, and HCT116 tumor cells with IC50 of 2.8, 3.20, and 3.25 μM, respectively. Moreover, 8f showed good antiproliferative activity against a panel of tumor cells.
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Affiliation(s)
- Bin Wang
- Department of Biochemistry and Molecular Biology, Sanquan College of Xinxiang Medical University, Xinxiang 453003, China; (B.W.); (L.Z.); (Y.W.)
| | - Youcai Liu
- Experimental Teaching Center of Biology & Basic Medicine, Sanquan College of Xinxiang Medical University, Xinxiang 453003, China;
| | - Lejing Zhang
- Department of Biochemistry and Molecular Biology, Sanquan College of Xinxiang Medical University, Xinxiang 453003, China; (B.W.); (L.Z.); (Y.W.)
| | - Yajuan Wang
- Department of Biochemistry and Molecular Biology, Sanquan College of Xinxiang Medical University, Xinxiang 453003, China; (B.W.); (L.Z.); (Y.W.)
| | - Zhaoxi Li
- Department of Biochemistry and Molecular Biology, Sanquan College of Xinxiang Medical University, Xinxiang 453003, China; (B.W.); (L.Z.); (Y.W.)
| | - Xin Chen
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Xianyang 712100, China
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46
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Ripa L, Sandmark J, Hughes G, Shamovsky I, Gunnarsson A, Johansson J, Llinas A, Collins M, Jung B, Novén A, Pemberton N, Mogemark M, Xiong Y, Li Q, Tångefjord S, Ek M, Åstrand A. Selective and Bioavailable HDAC6 2-(Difluoromethyl)-1,3,4-oxadiazole Substrate Inhibitors and Modeling of Their Bioactivation Mechanism. J Med Chem 2023; 66:14188-14207. [PMID: 37797307 DOI: 10.1021/acs.jmedchem.3c01269] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Histone deacetylase 6 (HDAC6) is a unique member of the HDAC family mainly targeting cytosolic nonhistone substrates, such as α-tubulin, cortactin, and heat shock protein 90 to regulate cell proliferation, metastasis, invasion, and mitosis in tumors. We describe the identification and characterization of a series of 2-(difluoromethyl)-1,3,4-oxadiazoles (DFMOs) as selective nonhydroxamic acid HDAC6 inhibitors. By comparing structure-activity relationships and performing quantum mechanical calculations of the HDAC6 catalytic mechanism, we show that potent oxadiazoles are electrophilic substrates of HDAC6 and propose a mechanism for the bioactivation. We also observe that the inherent electrophilicity of the oxadiazoles makes them prone to degradation in water solution and the generation of potentially toxic products cannot be ruled out, limiting the developability for chronic diseases. However, the oxadiazoles demonstrate high oral bioavailability and low in vivo clearance and are excellent tools for studying the role of HDAC6 in vitro and in vivo in rats and mice.
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Affiliation(s)
- Lena Ripa
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Jenny Sandmark
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Glyn Hughes
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Igor Shamovsky
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Anders Gunnarsson
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Julia Johansson
- Clinical Pharmacology and Safety Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Antonio Llinas
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Mia Collins
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Bomi Jung
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Anna Novén
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Nils Pemberton
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Mickael Mogemark
- Clinical Pharmacology and Safety Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Yao Xiong
- Pharmaron Beijing, Co. Ltd., No. 6, Taihe Road, BDA, Beijing 100176, China
| | - Qing Li
- Pharmaron Beijing, Co. Ltd., No. 6, Taihe Road, BDA, Beijing 100176, China
| | - Stefan Tångefjord
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Margareta Ek
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Annika Åstrand
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
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47
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Li Y, Liu S, Xu X, Xu J, Yang L, Hu L. Integrated molecular modeling and dynamics approaches revealed the mechanism of selective inhibition of HDAC6/8. J Biomol Struct Dyn 2023:1-14. [PMID: 37870047 DOI: 10.1080/07391102.2023.2272751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023]
Abstract
The high structural homology of histone deacetylases 6 and 8 (HDAC6/8) poses a challenge in achieving isoform selectivity and has resulted in adverse side effects due to pan-inhibition in clinical applications. Additionally, the rational design of dual-target inhibitors, centered on HDAC6/8, demands a profound understanding of their selectivity mechanisms. Addressing the urgent need for enhanced specificity in the development of inhibitors targeting specific isoforms, we elucidate the mechanism underpinning the selective inhibition of HDAC6/8 inhibitors through in-silico strategies. The hydrogen bonding interaction with Asp101 and Tyr306 is a key factor that enables compound 12b to selectively inhibit HDAC8. Its favorable spatial orientation places the Cap group of 12b between Tyr306 and Tyr100, resulting in an overall L-shaped conformation. These two factors significantly contribute to the selective inhibitory activity of 12b against HDAC8. The zinc binding group (ZBG) of compound NN-390 forms a hydrogen bond with His610, a key residue of HDAC6, facilitating stable chelation with zinc ions. In addition, the Cap group of NN-390 interacts with Phe620 and Phe680 via van der Waals forces, leading to an overall Y-shaped conformation. The aforementioned factors are the main reasons for the selective inhibition of HDAC6 by NN-390. Furthermore, whether the Cap group is in the para or meta-position will influence the selective inhibition of either HDAC6 or HDAC8. We believe these clues can offer valuable insights for the rational design of selective inhibitors targeting HDAC6/8 and pave the way for rational design of dual-target HDAC6/8-based inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yaxin Li
- Beijing Key Laboratory of Environmental and Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing, China
- Hebei Key Laboratory of Neuropharmacology, Department of Pharmacy, Hebei North University, Zhangjiakou, China
| | - Sisi Liu
- Hebei Key Laboratory of Neuropharmacology, Department of Pharmacy, Hebei North University, Zhangjiakou, China
| | - Ximing Xu
- Marine Biomedical Research Institute of Qingdao, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Qingdao Marine Science and Technology Center, Qingdao, China
| | - Jiamin Xu
- Beijing Key Laboratory of Environmental and Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing, China
| | - Leifu Yang
- Beijing Key Laboratory of Environmental and Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing, China
| | - Liming Hu
- Beijing Key Laboratory of Environmental and Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing, China
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48
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König B, Watson PR, Reßing N, Cragin AD, Schäker-Hübner L, Christianson DW, Hansen FK. Difluoromethyl-1,3,4-oxadiazoles Are Selective, Mechanism-Based, and Essentially Irreversible Inhibitors of Histone Deacetylase 6. J Med Chem 2023; 66:13821-13837. [PMID: 37782298 PMCID: PMC10591924 DOI: 10.1021/acs.jmedchem.3c01345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Histone deacetylase 6 (HDAC6) is an important drug target in oncological and non-oncological diseases. Most available HDAC6 inhibitors (HDAC6i) utilize hydroxamic acids as a zinc-binding group, which limits therapeutic opportunities due to its genotoxic potential. Recently, difluoromethyl-1,3,4-oxadiazoles (DFMOs) were reported as potent and selective HDAC6i but their mode of inhibition remained enigmatic. Herein, we report that DFMOs act as mechanism-based and essentially irreversible HDAC6i. Biochemical data confirm that DFMO 6 is a tight-binding HDAC6i capable of inhibiting HDAC6 via a two-step slow-binding mechanism. Crystallographic and mechanistic experiments suggest that the attack of 6 by the zinc-bound water at the sp2 carbon closest to the difluoromethyl moiety followed by a subsequent ring opening of the oxadiazole yields deprotonated difluoroacetylhydrazide 13 as active species. The strong anionic zinc coordination of 13 and the binding of the difluoromethyl moiety in the P571 pocket finally result in an essentially irreversible inhibition of HDAC6.
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Affiliation(s)
- Beate König
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Paris R Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Nina Reßing
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Abigail D Cragin
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Linda Schäker-Hübner
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Finn K Hansen
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
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49
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Watson PR, Stollmaier JG, Christianson DW. Crystal structure of histone deacetylase 6 complexed with (R)-lipoic acid, an essential cofactor in central carbon metabolism. J Biol Chem 2023; 299:105228. [PMID: 37703993 PMCID: PMC10622836 DOI: 10.1016/j.jbc.2023.105228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/28/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
The enzyme cofactor (R)-lipoic acid plays a critical role in central carbon metabolism due to its catalytic function in the generation of acetyl-CoA, which links glycolysis with the tricarboxylic acid cycle. This cofactor is also essential for the generation of succinyl CoA within the tricarboxylic acid cycle. However, the biological functions of (R)-lipoic acid extend beyond metabolism owing to its facile redox chemistry. Most recently, the reduced form of (R)-lipoic acid, (R)-dihydrolipoic acid, has been shown to inhibit histone deacetylases (HDACs) with selectivity for the inhibition of HDAC6. Here, we report the 2.4 Å-resolution X-ray crystal structure of the complex between (R)-dihydrolipoic acid and HDAC6 catalytic domain 2 from Danio rerio, and we report a dissociation constant (KD) of 350 nM for this complex as determined by isothermal titration calorimetry. The crystal structure illuminates key affinity determinants in the enzyme active site, including thiolate-Zn2+ coordination and S-π interactions in the F583-F643 aromatic crevice. This study provides the first visualization of the connection between HDAC function and the biological response to oxidative stress: the dithiol moiety of (R)-dihydrolipoic acid can serve as a redox-regulated pharmacophore capable of simultaneously targeting the catalytic Zn2+ ion and the aromatic crevice in the active site of HDAC6.
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Affiliation(s)
- Paris R Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Juana Goulart Stollmaier
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States.
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50
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Lambona C, Zwergel C, Fioravanti R, Valente S, Mai A. Histone deacetylase 10: A polyamine deacetylase from the crystal structure to the first inhibitors. Curr Opin Struct Biol 2023; 82:102668. [PMID: 37542907 DOI: 10.1016/j.sbi.2023.102668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/07/2023]
Abstract
Polyamine deacetylase activity was discovered more than 40 years ago, but the responsible histone deacetylase 10 (HDAC10) was described only recently. HDAC10 is a class IIb HDAC, as is its closest relative, the α-tubulin deacetylase HDAC6. HDAC10 has attracted attention over the last 2 years due to its role in diseases, especially cancer. This review summarises chemical and structural biology approaches to the study of HDAC10. Light will be shed on recent advances in understanding the complex structural biology of HDAC10 and the discovery of the first highly selective HDAC10 inhibitors.
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Affiliation(s)
- Chiara Lambona
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Rossella Fioravanti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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